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Tuesday, July 22, 2014

Genome editing excises HIV

The Scientist: ... The researchers, led by Kamel Khalili at Temple University in Philadelphia, Pennsylvania, used the CRISPR/Cas9 genome-editing system to excise HIV from several human cell lines, including microglia and T cells. They targeted both the 5’ and 3’ ends of the virus, called the long terminal repeats (LTRs), so that the entire viral genome was removed.

“We were extremely happy with the outcome,” Khalili told The Scientist. “It was a little bit . . . mind-boggling how this system really can identify a single copy of the virus in a chromosome, which is highly packed DNA, and exactly cleave that region.”

His team showed that not only could Cas9 excise one copy of the HIV genome, but—operating in the same cell—it could also clip out another copy lurking in a different chromosome. Often, Khalili said, a cell can have several copies of latent HIV distributed across various chromosomes. “Most likely the technology is going to clean up the viral DNA” in a cell, he said.

... One limitation of the CRISPR/Cas9 approach is that it can chop up unintended regions of the genome, producing so-called off-target effects. Khalili’s group performed whole-genome sequencing to look for off-target effects, but didn’t find any. T.J. Cradick, the director of the protein engineering core facility at Georgia Tech, said that a more thorough analysis of potential off-target effects is still required to make sure nothing has been overlooked. Nonetheless, “latent HIV provirus is a very exciting target and . . . a very promising way forward,” said Cradick, who did not participate in the study.

I felt guilty replying before reading the paper, so here is an update:

Fig.1 makes it very clear that only a subset of cells was successfully targeted (also, Fig.2C - a mere 3-fold reduction of viral production).

The claimed "no off-target effects" is basically bullshit: 1) looking at "predicted/potential off-target regions" tells you nothing because the bulk of non-specific effects is expected to be in the near random sequences (for the reason of expected specificity/abundance ratio), 2) the whole genome sequencing actually detected hundreds of thousands of mutations, but it was not clear (due to the way it was done) what proportion of them was to do CAS9. Attempt to to resolve this ambiguity again centered on predicted sequences, which is a joke.